# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 17:07:31 2021
#   Inital geometry file: a 93 line input string
#   Ligand name: (2S)-2-amino-4-oxo-4-[(2R)-2-phenylpyrrolidin-1-yl]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(=O)N1CCC[C@@H]1c2ccccc2)C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 M6J  M6J  '(2S)-2-amino-4-oxo-4-[(2R)-2-phenylpyrrolidin-1-yl]butanoic acid'  L-peptide  37  19  .  2022-07-25  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_M6J
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 M6J  C13  C  CH2   0  -0.452  67.9245  -24.5737  200.2185
 M6J  C15  C  CR6   0   0.141  67.6449  -26.7226  198.9035
 M6J  C17  C  CR16  0  -0.238  66.0158  -28.5013  198.7799
 M6J  C20  C  CR16  0  -0.303  67.4589  -26.4894  197.5430
 M6J  C04  C  C     0   0.544  72.2569  -29.4024  198.5065
 M6J  C06  C  CH1   0  -0.199  71.8856  -28.7460  199.8221
 M6J  C07  C  CH2   0  -0.590  70.5983  -27.9406  199.6423
 M6J  C11  C  CH2   0  -0.272  68.5054  -25.9204  202.1057
 M6J  C12  C  CH2   0  -0.489  67.4024  -25.0074  201.5827
 M6J  C14  C  CR15  0  -0.167  68.6018  -25.8402  199.6747
 M6J  C16  C  CR16  0  -0.305  66.9179  -27.7400  199.5135
 M6J  C18  C  CR16  0  -0.268  65.8313  -28.2568  197.4265
 M6J  C19  C  CR16  0  -0.242  66.5583  -27.2471  196.8084
 M6J  N10  N  NR5   0  -0.477  69.1123  -26.4618  200.8905
 M6J  N21  N  NH2   0  -0.800  72.9627  -27.8733  200.2416
 M6J  O09  O  O     0  -0.504  70.4483  -27.8498  202.0355
 M6J  H1   H  HCH2  0   0.252  68.6749  -23.7887  200.3338
 M6J  H2   H  HCH2  0   0.260  67.1479  -24.2012  199.5520
 M6J  H3   H  HCR6  0   0.255  65.4593  -29.2897  199.2702
 M6J  H4   H  HCR6  0   0.250  68.0285  -25.7095  197.0499
 M6J  H9   H  HCH1  0   0.259  71.6828  -29.5661  200.5266
 M6J  H10  H  HCH2  0   0.277  70.7857  -27.1266  198.9384
 M6J  H11  H  HCH2  0   0.293  69.8170  -28.5590  199.1924
 M6J  H12  H  HCH2  0   0.251  68.1242  -26.7202  202.7423
 M6J  H13  H  HCH2  0   0.246  69.2470  -25.3603  202.6809
 M6J  H14  H  HCH2  0   0.260  67.2190  -24.1678  202.2516
 M6J  H15  H  HCH2  0   0.242  66.4634  -25.5554  201.4808
 M6J  H16  H  HCR5  0   0.277  69.4283  -25.5593  199.0177
 M6J  H17  H  HCR6  0   0.254  67.0551  -27.9535  200.5664
 M6J  H18  H  HCR6  0   0.255  65.1307  -28.8513  196.8548
 M6J  H19  H  HCR6  0   0.256  66.4288  -27.0526  195.7515
 M6J  H30  H  HNH2  0   0.355  72.7598  -27.5449  201.1768
 M6J  H5   H  HNH2  0   0.352  73.8243  -28.3987  200.3192
 M6J  OXT  O  OH1   0  -0.594  71.3235  -30.2559  198.1028
 M6J  HXT  H  HOH1  0   0.484  71.5819  -30.6523  197.2575
 M6J  C08  C  C     0   0.572  70.0597  -27.4119  200.9581
 M6J  O05  O  O     0  -0.434  73.2768  -29.2014  197.8983

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 M6J  C13  C14  single    1.536  0.020  1.536
 M6J  C13  C12  single    1.524  0.020  1.524
 M6J  C15  C20  aromatic  1.393  0.020  1.393
 M6J  C15  C16  aromatic  1.391  0.020  1.391
 M6J  C15  C14  single    1.513  0.020  1.513
 M6J  C17  C18  aromatic  1.388  0.020  1.388
 M6J  C17  C16  aromatic  1.390  0.020  1.390
 M6J  C20  C19  aromatic  1.387  0.020  1.387
 M6J  C04  O05  double    1.204  0.020  1.204
 M6J  C04  C06  single    1.516  0.020  1.516
 M6J  C06  C07  single    1.529  0.020  1.529
 M6J  C06  N21  single    1.448  0.020  1.448
 M6J  C07  C08  single    1.517  0.020  1.517
 M6J  C08  N10  single    1.343  0.020  1.343
 M6J  C08  O09  double    1.226  0.020  1.226
 M6J  C11  N10  single    1.462  0.020  1.462
 M6J  C11  C12  single    1.524  0.020  1.524
 M6J  C14  N10  single    1.458  0.020  1.458
 M6J  C18  C19  aromatic  1.389  0.020  1.389
 M6J  C13  H1   single    0.970  0.020  1.090
 M6J  C13  H2   single    0.970  0.020  1.090
 M6J  C17  H3   single    0.930  0.020  1.080
 M6J  C20  H4   single    0.930  0.020  1.080
 M6J  C06  H9   single    0.970  0.020  1.090
 M6J  C07  H10  single    0.970  0.020  1.090
 M6J  C07  H11  single    0.970  0.020  1.090
 M6J  C11  H12  single    0.970  0.020  1.090
 M6J  C11  H13  single    0.970  0.020  1.090
 M6J  C12  H14  single    0.970  0.020  1.090
 M6J  C12  H15  single    0.970  0.020  1.090
 M6J  C14  H16  single    0.970  0.020  1.090
 M6J  C16  H17  single    0.930  0.020  1.080
 M6J  C18  H18  single    0.930  0.020  1.080
 M6J  C19  H19  single    0.930  0.020  1.080
 M6J  N21  H30  single    0.890  0.020  1.040
 M6J  N21  H5   single    0.890  0.020  1.040
 M6J  C04  OXT  single    1.328  0.020  1.328
 M6J  OXT  HXT  single    0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 M6J  H2   C13  H1   107.98  3.000
 M6J  H2   C13  C14  112.32  3.000
 M6J  H1   C13  C14  109.09  3.000
 M6J  H2   C13  C12  113.64  3.000
 M6J  H1   C13  C12  110.22  3.000
 M6J  C14  C13  C12  103.50  3.000
 M6J  C16  C15  C14  122.24  3.000
 M6J  C14  C15  C20  118.99  3.000
 M6J  C16  C15  C20  118.75  3.000
 M6J  H3   C17  C18  120.11  3.000
 M6J  H3   C17  C16  119.59  3.000
 M6J  C18  C17  C16  120.31  3.000
 M6J  H4   C20  C19  119.54  3.000
 M6J  H4   C20  C15  119.64  3.000
 M6J  C19  C20  C15  120.82  3.000
 M6J  OXT  C04  O05  123.31  3.000
 M6J  OXT  C04  C06  111.71  3.000
 M6J  O05  C04  C06  124.97  3.000
 M6J  H9   C06  N21  113.63  3.000
 M6J  H9   C06  C07  108.22  3.000
 M6J  N21  C06  C07  110.04  3.000
 M6J  H9   C06  C04  106.15  3.000
 M6J  N21  C06  C04  109.27  3.000
 M6J  C07  C06  C04  109.40  3.000
 M6J  H11  C07  H10  106.20  3.000
 M6J  H11  C07  C08  107.48  3.000
 M6J  H10  C07  C08  111.11  3.000
 M6J  H11  C07  C06  110.62  3.000
 M6J  H10  C07  C06  108.90  3.000
 M6J  C08  C07  C06  112.37  3.000
 M6J  H13  C11  H12  107.79  3.000
 M6J  H13  C11  N10  110.21  3.000
 M6J  H12  C11  N10  111.01  3.000
 M6J  H13  C11  C12  111.38  3.000
 M6J  H12  C11  C12  112.74  3.000
 M6J  N10  C11  C12  103.71  3.000
 M6J  H15  C12  H14  107.42  3.000
 M6J  H15  C12  C11  110.70  3.000
 M6J  H14  C12  C11  111.90  3.000
 M6J  H15  C12  C13  110.73  3.000
 M6J  H14  C12  C13  112.84  3.000
 M6J  C11  C12  C13  103.28  3.000
 M6J  H16  C14  N10  110.26  3.000
 M6J  H16  C14  C15  108.77  3.000
 M6J  N10  C14  C15  113.45  3.000
 M6J  H16  C14  C13  109.55  3.000
 M6J  N10  C14  C13  102.17  3.000
 M6J  C15  C14  C13  112.49  3.000
 M6J  H17  C16  C17  119.16  3.000
 M6J  H17  C16  C15  120.28  3.000
 M6J  C17  C16  C15  120.55  3.000
 M6J  H18  C18  C19  120.20  3.000
 M6J  H18  C18  C17  120.31  3.000
 M6J  C19  C18  C17  119.49  3.000
 M6J  H19  C19  C18  120.15  3.000
 M6J  H19  C19  C20  119.78  3.000
 M6J  C18  C19  C20  120.07  3.000
 M6J  C14  N10  C11  112.94  3.000
 M6J  C14  N10  C08  126.19  3.000
 M6J  C11  N10  C08  120.85  3.000
 M6J  H5   N21  H30  105.56  3.000
 M6J  H5   N21  C06  110.03  3.000
 M6J  H30  N21  C06  108.32  3.000
 M6J  HXT  OXT  C04  109.93  3.000
 M6J  O09  C08  N10  121.35  3.000
 M6J  O09  C08  C07  121.68  3.000
 M6J  N10  C08  C07  116.95  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 M6J  CONST_01  C18  C19  C20  C15    0.00   0.0  0
 M6J  CONST_02  C18  C17  C16  C15    0.00   0.0  0
 M6J  CONST_03  C20  C19  C18  C17    0.00   0.0  0
 M6J  CONST_04  C20  C15  C16  C17    0.00   0.0  0
 M6J  CONST_05  C19  C20  C15  C16    0.00   0.0  0
 M6J  CONST_06  C19  C18  C17  C16    0.00   0.0  0
 M6J  CONST_07  C14  C15  C16  C17  180.00   0.0  0
 M6J  CONST_08  C19  C20  C15  C14  180.00   0.0  0
 M6J  CONST_09  H19  C19  C20  C15  180.00   0.0  0
 M6J  CONST_10  H3   C17  C16  C15  180.00   0.0  0
 M6J  CONST_11  H17  C16  C15  C20  180.00   0.0  0
 M6J  CONST_12  H18  C18  C19  C20  180.00   0.0  0
 M6J  CONST_13  H4   C20  C15  C14    0.00   0.0  0
 M6J  CONST_14  C11  N10  C08  C07  180.00   0.0  0
 M6J  CONST_15  C14  N10  C08  C07    0.00   0.0  0
 M6J  CONST_16  O09  C08  N10  C11    0.00   0.0  0
 M6J  CONST_17  O09  C08  N10  C14  180.00   0.0  0
 M6J  CONST_18  HXT  OXT  C04  C06  180.00   0.0  0
 M6J  Var_01    N10  C11  C12  C13  -27.94  30.0  1
 M6J  Var_02    C14  C13  C12  C11   38.05  30.0  1
 M6J  Var_03    C14  N10  C11  C12    7.34  30.0  1
 M6J  Var_04    N10  C08  C07  C06  165.94  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 M6J  chir_01  C06  C04  C07  N21  positiv
 M6J  chir_02  C14  N10  C13  C15  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 M6J  plan-1  C15  0.020
 M6J  plan-1  C17  0.020
 M6J  plan-1  C20  0.020
 M6J  plan-1  C14  0.020
 M6J  plan-1  C16  0.020
 M6J  plan-1  C18  0.020
 M6J  plan-1  C19  0.020
 M6J  plan-1  H3   0.020
 M6J  plan-1  H4   0.020
 M6J  plan-1  H17  0.020
 M6J  plan-1  H18  0.020
 M6J  plan-1  H19  0.020
 M6J  plan-2  C07  0.020
 M6J  plan-2  C11  0.020
 M6J  plan-2  C14  0.020
 M6J  plan-2  N10  0.020
 M6J  plan-2  O09  0.020
 M6J  plan-2  C08  0.020
 M6J  plan-3  C04  0.020
 M6J  plan-3  C06  0.020
 M6J  plan-3  OXT  0.020
 M6J  plan-3  HXT  0.020
 M6J  plan-3  O05  0.020

